Structure of PDB 7uk7 Chain A Binding Site BS01

Receptor Information
>7uk7 Chain A (length=389) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHMLRHNVPVRRDLDQIAADNGFDFHIIDNEIYWDESRAYRFTLRQIEEQ
IEKPTAELHQMCLEVVDRAVKDEEILTQLAIPPLYWDVIAESWRARDPSL
YGRMDFAWCGNAPVKLLEYNADTPTSLYESAYFQWLWLEDARRSGIIPRD
ADQYNAIQERLISRFSELYSREPFYFCCCQDTDEDRSTVLYLQDCAQQAG
QESRFIYIEDLGLGVGGVLTDLDDNVIQRAFKLYPLEWMMRDDNGPLLRK
RREQWVEPLWKSILSNKGLMPLLWRFFPGHPNLLASWFDGEKPQIAAGES
YVRKPIYSREGGNVTIFDGKNNVVDHADGDYADEPMIYQAFQPLPRFGDS
YTLIGSWIVDDEACGMGIREDNTLITKDTSRFVPHYIAG
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7uk7 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7uk7 Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		L115 E116 K265 V300 K302 R307 E308 G309 Q337 F339 Q340 L372 I373 T374
Binding residue
(residue number reindexed from 1)		L117 E118 K267 V302 K304 R309 E310 G311 Q339 F341 Q342 L374 I375 T376
Annotation score4
Enzymatic activity
Enzyme Commision number 6.3.1.-
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7uk7, PDBe:7uk7, PDBj:7uk7
PDBsum7uk7
PubMed36745518
UniProtP33222|YJFC_ECOLI Putative acid--amine ligase YjfC (Gene Name=yjfC)

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